Comammox Nitrospira bacteria outnumber canonical nitrifiers irrespective of electron donor mode and availability

Complete ammonia oxidizing bacteria coexist with canonical ammonia and nitrite oxidizing bacteria in a wide range of environments. Whether this coexistence is due to competitive or cooperative interactions between the three guilds, or a result of niche separation is not yet clear. Understanding the factors driving coexistence of nitrifying guilds is critical to effectively manage nitrification processes occurring in engineered and natural ecosystems. In this study, microcosms-based experiments were used to investigate the impact of electron donor mode (i.e., ammonia and urea) and loading on the population dynamics of nitrifying guilds in drinking water biofilter media. Shotgun sequencing of DNA from select time points followed by co-assembly and re-construction of metagenome assembled genomes (MAGs) revealed multiple clade A2 and one clade A1 comammox bacterial populations coexisted in the microcosms alongside Nitrosomonas-like ammonia oxidizers and Nitrospira-like nitrite oxidizer populations. Clade A2 comammox bacteria were likely the primary nitrifiers within the microcosms and increased in abundance over canonical ammonia and nitrite oxidizing bacteria irrespective of electron donor mode or nitrogen loading rates. This suggests that comammox bacteria will outnumber nitrifying communities sourced from oligotrophic environments irrespective of variable nitrogen regimes. Changes in comammox bacterial abundance were not correlated with either ammonia or nitrite oxidizing bacterial abundance in urea amended systems where metabolic reconstruction indicated potential cross feeding between ammonia and nitrite oxidizing bacteria. In contrast, comammox bacterial abundance demonstrated a negative correlation with that of nitrite oxidizers in ammonia amended systems. This suggests that potentially weaker synergistic relationships between ammonia and nitrite oxidizers might enable comammox bacteria to displace nitrite oxidizers from complex nitrifying communities.

Disturbance-based management of ecosystem services and disservices in partial nitritation anammox biofilms

The resistance and resilience provided by functional redundancy, a common feature of microbial communities, is not always advantageous. An example is nitrite oxidation in partial nitritation-anammox (PNA) reactors during wastewater treatment, where suppression of nitrite oxidizers like Nitrospira is sought. In these ecosystems, biofilms provide microhabitats with oxygen gradients, allowing the coexistence aerobic and anaerobic bacteria. We designed a disturbance experiment where PNA biofilms treating water from a high rate activated sludge process removing organic matter (mainstream wastewater), were constantly or intermittently exposed to the effluent of anaerobic sewage sludge digestion dewatering (sidestream wastewater), which has been proposed to inhibit nitrite oxidizers. With increasing sidestream exposure we observed decreased abundance, alpha-diversity, functional versatility, and hence functional redundancy, among Nitrospira in the PNA biofilms, while the opposite patterns were observed for anammox bacteria within Brocadia. At the same time, species turnover was observed for the aerobic ammonia-oxidizing Nitrosomonas populations. The different exposure regimens were associated with metagenomic assembled genomes of Nitrosomonas, Nitrospira, and Brocadia, encoding genes related to N-cycling, substrate usage, and osmotic stress response, possibly explaining the three different patterns by niche differentiation. These findings imply that disturbances can be used to manage the functional redundancy of biofilm microbiomes in a desirable direction, which should be considered when designing operational strategies for wastewater treatment.

Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean

Ammonia oxidation to nitrite and its subsequent oxidation to nitrate provides energy to the two populations of nitrifying chemoautotrophs in the energy-starved dark ocean, driving a coupling between reduced inorganic nitrogen (N) pools and production of new organic carbon (C) in the dark ocean. However, the relationship between the flux of new C production and the fluxes of N of the two steps of oxidation remains unclear. Here, we show that, despite orders-of-magnitude difference in cell abundances between ammonia oxidizers and nitrite oxidizers, the two populations sustain similar bulk N-oxidation rates throughout the deep waters with similarly high affinities for ammonia and nitrite under increasing substrate limitation, thus maintaining overall homeostasis in the oceanic nitrification pathway. Our observations confirm the theoretical predictions of a redox-informed ecosystem model. Using balances from this model, we suggest that consistently low ammonia and nitrite concentrations are maintained when the two populations have similarly high substrate affinities and their loss rates are proportional to their maximum growth rates. The stoichiometric relations between the fluxes of C and N indicate a threefold to fourfold higher C-fixation efficiency per mole of N oxidized by ammonia oxidizers compared to nitrite oxidizers due to nearly identical apparent energetic requirements for C fixation of the two populations. We estimate that the rate of chemoautotrophic C fixation amounts to ∼1 × 1013to ∼2 × 1013mol of C per year globally through the flux of ∼1 × 1014to ∼2 × 1014mol of N per year of the two steps of oxidation throughout the dark ocean.

High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant

Nitrification, the oxidation of ammonia to nitrate via nitrite, is an important process in municipal wastewater treatment plants (WWTPs). Members of the Nitrospira genus that contribute to complete ammonia oxidation (comammox) have only recently been discovered and their relevance to engineered water treatment systems is poorly understood. This study investigated distributions of Nitrospira, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in biofilm samples collected from tertiary rotating biological contactors (RBCs) of a municipal WWTP in Guelph, Ontario, Canada. Using quantitative PCR (qPCR), 16S rRNA gene sequencing, and metagenomics, our results demonstrate that Nitrospira species strongly dominate RBC biofilm samples and that comammox Nitrospira outnumber all other nitrifiers. Genome bins recovered from assembled metagenomes reveal multiple populations of comammox Nitrospira with distinct spatial and temporal distributions, including several taxa that are distinct from previously characterized Nitrospira members. Diverse functional profiles imply a high level of niche heterogeneity among comammox Nitrospira, in contrast to the sole detected AOA representative that was previously cultivated and characterized from the same RBC biofilm. Our metagenome bins also reveal two cyanase-encoding populations of comammox Nitrospira, suggesting an ability to degrade cyanate, which has not been shown previously for Nitrospira that are not strict nitrite oxidizers. This study demonstrates the importance of RBCs as model systems for continued investigation of environmental factors that control the distributions and activities of AOB, AOA, comammox Nitrospira, and other nitrite oxidizers.

Discovery of New Nitrite-Oxidizing Bacteria Increases Phylogenetic and Metabolic Diversity within This Niche

ABSTRACTK. Kitzinger et al. (mBio 9:e01186-18, 2018, https://doi.org/10.1128/mBio.01186-18) report the first isolation of a novel nitrite-oxidizing bacterium, “CandidatusNitrotoga,” and provide the first detailed information on the physiology, phylogeny, and characterization of the nitrite-oxidizing system of this genus. The isolate was derived from a wastewater treatment system and exhibits adaptation and tolerance to relatively high levels of nitrite. The origin of its nitrite oxidoreductase is distinct from other known nitrite oxidoreductase (NXR) systems, having arisen either in this organism or by horizontal gene transfer. In contrast to many earlier-characterized nitrite oxidizers, it displays substantial metabolic plasticity in its mode of energetic metabolism with capabilities to use both hydrogen and sulfite as electron donors.

Niche differentiation of ammonia and nitrite oxidizers along a salinity gradient from the Pearl River estuary to the South China Sea

The niche differentiation of ammonia and nitrite oxidizers is controversial because they display disparate patterns in estuarine, coastal, and oceanic regimes. We analyzed diversity and abundance of ammonia-oxidizing archaea (AOA) and β-proteobacteria (AOB), nitrite-oxidizing bacteria (NOB), and nitrification rates to identify their niche differentiation along a salinity gradient from the Pearl River estuary to the South China Sea. AOA were generally more abundant than β-AOB; however, AOB more clearly attached to particles compared with AOA in the upper reaches of the Pearl River estuary. The NOB Nitrospira had higher abundances in the upper and middle reaches of the Pearl River estuary, while Nitrospina was dominant in the lower estuary. In addition, AOB and Nitrospira could be more active than AOA and Nitrospina since significantly positive correlations were observed between their gene abundance and the nitrification rate in the Pearl River estuary. There is a significant positive correlation between ammonia and nitrite oxidizer abundances in the hypoxic waters of the estuary, suggesting a possible coupling through metabolic interactions between them. Phylogenetic analysis further revealed that the AOA and NOB Nitrospina subgroups can be separated into different niches based on their adaptations to substrate levels. Water mass mixing is apparently crucial in regulating the distribution of nitrifiers from the estuary to open ocean. However, when eliminating water mass effect, the substrate availability and the nitrifiers' adaptations to substrate availability via their ecological strategies essentially determine their niche differentiation.